Structures of enzymes from the histidine biosynthesis pathway of E. coli. (a) l-Histidinol phosphate aminotransferase (HisC) dimer as bound to PMP (PDB code 1FG7). The small domain (blue) and large domain (green) containing bound pyridoxamine-5′-phosphate (PMP, red) are depicted. This enzyme catalyzes the seventh step in the histidine biosynthesis pathway. Structures were determined with bound PMP and PLP as well as with both l-histidinol phosphate and PLP, the latter structure resembling a gem-diamine intermediate (57). (b) l-Histidinol dehydrogenase dimer bound to Zn²⁺, l-histidinol, and NAD (PDB code 1KAE). The two larger domains, 1 (blue) and 2 (green), contain a Rossmann fold, with domain 3 (magenta) containing a three-stranded β-sheet and 4 (sky blue) a two-helix hairpin. The ligands Zn²⁺ (yellow) and NAD/l-histidinol (red) are depicted in ball-and-stick representation. The HisD structure and its complexes revealed the role of Zn²⁺ in substrate binding, a gene duplication event leading to two incomplete Rossmann fold domains, and the roles of His327 and Glu326 in catalysis (4). These and subsequent figures were prepared with the program Molscript (18) and rendered with Raster3D (39).

Structure of carbohydrate-processing enzymes from E. coli. (a) Ribose-5-phosphate isomerase RpiA dimer (PDB code 1LKZ), with the small domain (green) and large domain (blue) shown. The structure revealed a dimeric enzyme, with each monomer having two domains (49). The putative active-site residues Asp81, Asp84, and Lys94 cluster near the active-site cleft. (b) Glucose-1-phosphate thymidyltransferase RffH dimer (PDB code 1MC3). dTTP (red) and Mg²⁺ (sky blue) are depicted in ball-and-stick representation. The RffH structure adopts a dimer-of-dimers arrangement (59). The Mg²⁺ ion within the active site serves to correctly orient the substrate molecules, thereby facilitating an S_N2 nucleophilic attack at the dTTP α-phosphate.

Histidine biosynthesis pathway of E. coli (71). Steps in the pathway for which enzyme structures have been determined are shown in shaded boxes.

Structures of E. coli rRNA binding and processing proteins. (a) Pseudouridine synthase RsuA (PDB code 1KSV), consisting of the rRNA-binding domain (blue) and catalytic module (green) bound to UMP (red). This structure (58) and its comparison with the structure of TruA (18) and the sequences of other pseudouridine synthases revealed a conserved fold for the catalytic module and similar active site for the four families of these enzymes. (b) The small conserved RNA-binding protein YbcJ (PDB code 1O09). The overall structure of this protein contains the αL motif (62) and resembles that of a domain of ribosomal protein S4. (c) 23S rRNA 2′-O-methyltransferase RlmB dimer (PDB code 1GZ0), with the rRNA-binding domain (blue) and catalytic domain (green) depicted. The rRNA-binding domain resembles that of ribosomal proteins L7 and L30, while the C-terminal domain containing the active site displays a novel methyltransferase fold with a deep knot (41).